The oculomotor system, which optimizes visual interaction with the environment, provides a valuable model system for probing the building blocks of higher-order cognition. Attention shifting, working memory, and inhibition of prepotent responses can be investigated in healthy individuals and patients with brain disorders. Although the neurophysiology of the oculomotor system has been well characterized at the single-cell level in nonhuman primates, its functional architecture in humans determined by evoked response procedures and studies of patients with focal lesions has been limited. Available evidence points to a widely distributed set of neocortical and subcortical brain regions involved in the control of eye movements, including brain stem, cerebellum, thalamus, striatum, and parietal and frontal cortices. The advent of functional magnetic resonance imaging provides a noninvasive manner of localizing, at high spatial resolution, the brain systems that subserve different aspects of sensory and cognitive processes in humans. Functional magnetic resonance imaging studies have already delineated the brain systems subserving sensorimotor and cognitive control of eye movements in adult and pediatric populations. Hence, the combination of functional magnetic resonance imaging and eye movement procedures can be used to probe the integrity of the brain in neurological and psychiatric disorders as well as provide a window into the changes in brain function subserving cognitive development.